Visium RNA Level 2
A 10x Visium RNA Level 2 entry documents the alignment workflow outputs downstream of a 10x Visium RNA Level 1 file. This level captures the SAM tags used for the unique molecular identifier (UMI) and spatial barcode fields, a link to the spatial barcode whitelist file, whether hard trimming was applied, and the genomic reference, genome annotation, and workflow version used to perform the alignment.
Level 2 entries make explicit how raw spatial reads were mapped and tagged with their spatial barcodes, preserving the technical details needed to reproduce or audit the alignment step before expression quantification.
Why You Should Contribute 10x Visium RNA Level 2 Entries¶
Contributing 10x Visium RNA Level 2 entries ensures that the alignment and barcode-tagging workflow applied to spatial sequencing reads is documented with enough detail for others to reproduce or evaluate the analysis shared through the CCKP.
Who Should Be Contributing 10x Visium RNA Level 2 Entries?¶
- Computational Genomics Analysts – Record alignment tags, genomic reference, and workflow versions used to process spatial reads.
- Bioinformatics Pipeline Developers – Document the spatial barcode whitelist and trimming parameters applied during alignment.
- Spatial Biology Researchers – Confirm that aligned outputs are correctly linked back to the raw Visium run they originated from.
- Data Managers – Maintain consistent, portal-ready metadata for aligned Visium sequencing outputs shared through the CCKP.
Download Template¶
You can download the VisiumRNALevel2 CSV template to streamline data entry.
Full Field Reference¶
Below is the full field reference table with attributes and their descriptions.
| Attribute | Description | Required | Column Type | Format | Regex Pattern | Standard Terms | Examples |
|---|---|---|---|---|---|---|---|
| 10xVisiumRNALevel2_id | Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated. | True | string | None | ^syn\d{7,8}$ | None | |
| Filename | The path of a file in Synapse, relative to the project. The file associated with the path will be annotated with attributes contained in this sheet. | False | string | None | None | None | |
| 10xVisiumRNALevel1 Key | Unique 10xVisiumRNALevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list. | False | string | None | None | None | |
| Biospecimen Key | Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list. | False | string | None | -B\d{1,9} | None | |
| Study Key | The unique Study_id foreign keys associated with the resource, found in the grant Study information. Used to group the resource with other components. Please provide multiple values as a comma-separated list. | False | string | None | None | None | |
| DatasetView Key | Unique DatasetView_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list. | False | string | None | None | None | |
| File Alias | A string identifier associated with the file. Must be unique. Can be the repository accesssion number (e.g., Synapse ID, GEO identifier such as GSE12345). No Greek Letters or DOIs. | True | string | None | None | None | |
| File Description | Description of the file. | False | string | None | None | None | |
| File Design | The overall design of the dataset or file, including a batch identifier, if applicable. | False | string | None | None | None | |
| File Level | The processing level the file can be mapped to. | True | string | None | None | View | |
| File Assay | The assay the file is representative of. | True | string | None | None | View | |
| File Species | The species the data was collected on. | True | string | None | None | View | |
| File Url | The url of where the file is stored. | True | string | uri | None | None | |
| File Format | The format of the file described by this entry. | True | string | None | None | View | |
| File Data Use Codes | DUO code - A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Available DUO code definitions can be found here: https://mc2-center.github.io/data-models/valid_values/study/#attribute-study-data-use-codes | False | string_list | None | None | None | |
| File Longitudinal Group | A label that can be used to identify groups of files from the same longitudinal/time-resolved experiment | False | string | None | None | None | |
| File Longitudinal Event Type | The type of event to which File Longitudinal Total Time Elapsed is related | False | string | None | None | View | |
| File Longitudinal Sequence Identifier | The order in which this file was collected with respect to the longitudinal experiment (e.g., 1, 2, etc.). Integer. | False | number | None | None | None | |
| File Longitudinal Time Elapsed Unit | The unit of time associated with Sequential and Total Time Elapsed attributes. | False | string | None | None | None | |
| File Longitudinal Total Time Elapsed | The total time elapsed between the first and current files contained this longitudinal group. | False | number | None | None | None | |
| Visium UMI Tag | SAM tag for the UMI field; please provide a valid tag-type pair, consisting of a tag (e.g. UB or UR) and type (e.g. Z) separated by a colon. | True | string | None | None | None | |
| Visium Whitelist Spatial Barcode File Link | Link to file listing all possible spatial barcodes. URL | True | string | None | None | None | |
| Visium Spatial Barcode Tag | SAM tag for spot barcode field; please provide a valid tag-type pair, consisting of a tag (e.g. CB or CR) and type (e.g. Z) separated by a colon. | True | string | None | None | None | |
| Visium Applied Hard Trimming | Was Hard Trimming applied | True | boolean | None | None | View | |
| Workflow Version | Major version of the workflow (e.g. Cell Ranger v3.1) | False | string | None | None | None | |
| Workflow Link | Link to documentation or webpage associated with the computational workflow used to generate the file. | False | string | uri | None | None | |
| Genomic Reference | Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39) | False | string | None | None | None | |
| Genomic Reference URL | Link to human genome sequence; ftp or reference URL will be accepted. | False | string | uri | None | None | |
| Genome Annotation URL | Link to the human genome annotation (GTF) file; ftp or reference URL will be accepted. | False | string | uri | None | None | |
| Visium Run ID | A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow. | True | string | None | None | None | |
| Visium Capture Area | Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1. | False | string | None | None | View |